Abstract: An Fe-based hydrodesulfurization (HDS) catalyst modified by Y zeolite was developed using Fe as the main active metal and Zn as a promoter. The change of morphology, pore structure, dispersity, reducibility, electronic defect structure and acidity of the Fe-based catalysts before and after modification were investigated using low-temperature nitrogen physical adsorption, X-ray diffraction (XRD), H₂-temperature programmed reduction (H₂-TPR), NH₃-temperature programmed desorption (NH₃-TPD), scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS) and pyridine infrared spectroscopy (Py-IR). Meanwhile, the HDS performance of the Fe-based catalyst was evaluated using a fixed-bed reactor. The results showed that the introduction of Y zeolite provided the Brønsted (B) acid sites, which increased the sulfur removal rates of Fe based catalysts by 10.7% −34.1%. Meanwhile, the B acid sites improved the selectivity of the direct desulfurization (DDS) reaction pathway. In addition, the B acid sites not only promoted the increase of DDS selectivity but also inhibited further deep hydrogenation of tetrahydrodibenzothiophene (THDBT) and hexahydrodibenzothiophene (HHDBT) in the hydrogenation (HYD) reaction pathway, thereby ensuring an increase in desulfurization efficiency while reducing hydrogen consumption. The fundamental reason was that the introduction of Y zeolite enhanced the acidity of the modified catalyst, especially the interaction between B acid sites and active metal promoted electron transfer, which adjusted the Fe species electronic defect structure, resulting in the improvement of HDS performance.